Hello colleagues,
I am wondering if it is possible to solve G-quadruplex structure by cryoEM technique...Please, do you have some experiences with it? Because to my best of knowledge, there are only RTG and NMR structures so far. Why?
Thanks for the answers
Martin
I would assume the problem is size - The smaller a particle is , the harder it is to distinguish from the background - Therefore there are cryo-EM structures of nucleosomes and ribosomes, but not of small snippets of DNA.
Thanks for the answer, professor Annemarie Honegger ,
it sounds logical, but recently I have found this structure:
CryoEM structure of the MDA5-dsRNA filament with 74-degree helical twist (
PDB: 6G19, 724 residues, y. 2018), so the size could be quite comparable with the size of G-quadruplex molecules.
Maybe, I should quite reformulate my question. Is it possible to solve some specific DNA structures (G-quadruplex, i-motif,...) by cryoEM? Because till date only "protein" or "mixed" structures are available. Has somebody tried to solve DNA itself by cryoEM?
Thanks
Martin
It certainly should be possible to solve pure DNA structures by CryoEM if they are both large enough and sufficiently structurally defined. I would expect to see cryo-EM structures of artificial DNA nanostructures, as these are in a size range appropriate for Cryo-EM structure determination. Actually a Google-scholar search for these search terms revealed for example:
https://www.pnas.org/content/pnas/109/49/20012.full.pdf (Cryo-EM structure of a 3D DNA-origami object)
https://www.nature.com/articles/nature02307 (A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron)
https://www.nature.com/articles/nature07971 (Self-assembly of a nanoscale DNA box with a controllable lid),
demonstrating that indeed it is possible to solve pure DNA structures by CryoEM
Hi Martin Bartas , In fact it should be much easier to solve DNA rather than protein because DNA has more heavy elements like Phosporus, Sulphur, Nitrogen etc. as compared to mostly Carbon, Hydrogen, Oxygen etc, in proteins. This would thus result in much more enhanced amplitude contrast at same defocus for DNA. Finally, this implies that you can get better resolution maps for DNA than protein (assuming other factors to be same, which is MOSTLY NOT the case) at same defocus.
Haaris Ahsan Safdari thank you very much for the encouragement, it sounds great! I will contact some cryoEM laboratories and try to design my experiment. Cheers!
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